Falling Into Darkness Slowly
by Jasmin Kenobi
Summary: *CONTAINS SPOILERS IF YOU HAVEN'T SEEN INTO DARKNESS YET* The Avengers have to team up with Starfleet and the USS Enterprise in order to stop one of the worst enemies they've ever met: John Harrison. But who is he really? And what's up with Admiral Marcus and his weird schemes? And what the hell is in those bloody torpedoes? It's up to the Avengers and the Enterprise to find out!


**AN- Hey y'all, I've decided to write the first chapter of an Into Darkness fic, while listening to the soundtrack on YouTube. This is the best way to get inspiration ever! Well, if you have no idea who some of these characters are, either look at my other stories or go to DeviantArt and find the profile ~ninjazzkat. I have a fanfiction there that will explain partially who some of these characters are. If you can't find anything there, just ask me! I'll be sure to answer your questions ASAP. Enough talking. Let's get to the fic!**

Chapter One- Falling Into Darkness Slowly

Virginia "Pepper" Potts was talking with her boyfriend, Tony Stark, when the news channel overrode their music that Pepper had on. She stared in shock at the report.

"_A Starfleet facility in London has been destroyed today in what Starfleet officials are calling a malfunction of the new computer core they had put in to store more data. The facility, known as the Kelvin Memorial Archive, was mainly used to store records on ships lost in action, such as the famed _U.S.S. Kelvin_, which was lost to a Romulan attack more than twenty five years ago._

_ "Starfleet officials state that they will undergo emergency situation protocols so that another attack like this cannot happen again. What are those procedures? Heightened security checks at all Starbases in the entire Federation, all ships on standby, and a highly classified meeting of Starfleet officials to discuss what they should do now to combat this threat._

_ "This reporter can only ask why Starfleet has not been this prepared in decades and whether this is a true terrorist threat or not?"_

"TONY!" Pepper yelled at the man as he came out of the bathroom. He seemed strained.

"I know, Pepper," he said, "Fury just informed all S.H.E.I.L.D. agents and Avengers that we are to help Starfleet Intelligence in any way possible. I've just been assigned to the _Enterprise_ to assist in helping them put in some new torpedoes that they might need to take down the guy who committed this atrocity. Sorry, Peps, but I have to catch the next shuttle to Starbase One."

Pepper nodded, tears in her eyes as she watched the footage of the explosion, "Take this guy down, Tony. Please. For all the people killed."

Tony nodded tersely and left. Moments later, Pepper heard the recognizable hum of a transporter as Tony's luggage was beamed up to the Starbase.

! #$%^&*())(*&^%$# !

General Jasmin Kenobi of the Galactic Republic Grand Army sat down at the table. The only people missing were Admiral Chris Pike and Commander James Kirk. Jasmin knew Jim was going to get his ass demoted one day for doing something stupid.

The pair walked in and sat down just as the meeting started.

Admiral Marcus stood, "I'm sure you all know what happened in London. The man who did it: one of our top agents. His name is John Harrison."

Marcus droned on and on, but Jasmin didn't pay attention. The young woman sitting next to her would very well fill her in later after reading her the riot act.

Said young woman was sitting straight-backed in her chair as the junior representative from the Republic in this matter. She was paying very good attention, which made Jasmin wonder what she was going to be in for later. She was gazing out the window when she felt a tremor in the Force. She jumped slightly in her seat. Her Padawan turned her head towards the window and proceeded to speak, her voice calm and measured.

"I believe Commander Kirk is right. We have felt the disturbance in the Force. It is very near to this room-" she was cut off as Jim stood in response to a red light and a humming sound that began suddenly.

Marcus stared at him, "I know that what Commander T'Mir said agrees with what you think, son, but that doesn't mean you need to stand up to speak."

Jim turned back to the meeting, "Clear the room!"

Jasmin and T'Mir both stood and ran over to the window, where an aerial craft waited, its weapons preparing to fire. They both pulled out their lightsabers, and three blades lit the room, combating the red glow in blue, green, and orange hues.

The craft began firing, and despite their skills in battle, Jasmin and her Padawan could do nothing as innocent people were shot on sight. Jasmin dove in front of Commander Spock as he moved in front of a table, which he should have rightly been hiding behind right now.

T'Mir struggled to protect Admiral Marcus as he retreated out of the room. The young Vulcan woman had knowledge with a lightsaber, but she was being pummeled by the craft's relentless barrage on her. Marcus was giving her orders that Jasmin couldn't hear. She watched in slow-motion as Chris Pike struggled to crawl across the floor to her and Spock, only to be shot in the chest. Spock leapt into action, pulling Pike across the floor and into the hallway, where Jasmin joined him.

She and Spock both knew he was going to die. There was nothing they could do. Tears blurred her vision as she cried in grief as she watched the man who was like a father to her slip away. She didn't even notice Spock's mind-meld with Pike. Only later would she remember that. She just tried to come to terms with the death of yet another person she had grown close to.

! #$%^&*())(*&^%$# !

Natasha Romanoff sat in the plaza below Starfleet Headquarters. She was talking with an Ensign Pavel Chekov in their native language, Russian, when the attack began. She shoved Chekov to the ground and covered him with her gun. He stared at her in surprise before diving for a hidden panel.

"My former roommate shoved me zis," he explained, "In case of an emergency, she said to grab a veapon from here and defend myself."

"Yeah, that sounds about right," Natasha said as she fired up at the craft. She saw the explosion and pulled Chekov away as the craft came plummeting to the ground right where they had been mere seconds ago. The young teenager stared with round eyes at the craft that had almost killed them. Starfleet Security officials had the vehicle surrounded in moments.

They were being questioned by the officials when Jasmin Kenobi came out of the building, her eyes red and puffy, but a murderous look on her face. Her apprentice, T'Mir Tucker, followed her. The human-Vulcan hybrid looked unusually worried as Natasha called her over.

"What happened up there?" Natasha demanded, ignoring the questions of the security goons behind her.

T'Mir looked down for a split second before answering, "Admiral Pike was killed in the attack."

Chekov looked like he had been punched, "He ees dead!?"

The security men had stopped speaking and pulled their hats off. The lead one murmured a quick prayer before turning to the trio.

"May he rest in peace. Knowing Kirk's reputation, kid, you just got put in a death row position. Kirk's gonna catch that sonuva bitch and make him pay."

Natasha sighed, "It's not him I'm worried about. It's the angry Jedi Master that just walked past. She is going to hunt that bastard down and kill him for what he did here. Trust me, you should have seen what she did to Loki in New York. She gave him a scar to remember, all because he killed one of her friends."

"My Master does have an unfortunate tendency to go through that stage of grief."

It was James Kirk who spoke next from behind the security guy, "She has six stages of grief: crying, getting a drink, hunting the bastard down, killing him, bringing his body back, then getting as hammered as she can possibly get."

Chekov's eyes went wide, "He vill kill her. Ve saw vhat he did! Vhat ees she zinking?"

"Her mind will focus on nothing but this sick bastard," Kirk said, "Now, if you will excuse me ladies, Ensigns. Chekov, I expect you at your post by 0600 tomorrow morning."

"Aye, Keptin," the young Russian replied. He looked to be in deep thought after Kirk left. He sighed before following Kirk to the transporter station.

Natasha shrugged. These crazy people were Stark's problem now. She was assigned to shadow Admiral Marcus along with Clint. She turned and walked away, leaving T'Mir to gaze up at the stars and wonder why John Harrison wanted to kill so many people.

! #$%^&*())(*&^%$# !

Lieutenant Nyota Uhura sat at her station when a man appeared behind her. He had a goatee and a smirk on his face. She could see his reflection on her display panel. He was wearing a suit, which was odd.

She spun in her chair, "May I help you, sir?"

He nodded quickly, "I was looking for Kirk. More like trying to avoid him. Do you know where he is?"

"On his way here from Sickbay," she said, turning to track the Captain's movements.

"Hide me!" the man hissed as Kirk stepped on the bridge. She covered him with her chair as she gave her report to Kirk. The man thanked her silently as Kirk sat down and he snuck into the lift. Kirk looked back at hearing the doors swish closed.

"Who was that?" he said to her, looking mildly amused.

"I don't know what you're talking about," she said as she turned her attention to her work.

When Nyota stepped into her quarters later, the man was there, wearing an engineering uniform. He appeared to be an ensign.

"Why are you here?" she asked heatedly.

"To thank you, Lieutenant Uhura. I didn't want Kirk to know I was here. I was assigned by Fury to be on this ship during this crisis situation. Do you know the name of the blond science officer? The new one?" he asked.

"She's Lieutenant Carol Wallace. And who are you?"

"Tony Stark. I answer to Iron Man as well," he said nonchalantly.

"I guess it is best the Captain doesn't know you're here. We're going near the Klingon Neutral Zone. Maybe you should play a new security officer. Pick a name," she suggested. If Stark was under orders, who was she to stop that?

"Um," he said, looking thoughtful, "Harry Potts. That was my girlfriend's dad's name."

"Alright, here let me put it in quickly," Nyota said as she slipped the name into the system and generated a profile from the S.H.E.I.L.D. database that Stark provided.

"Thanks," he said, "I guess I owe you big time now."

"A box of chocolates goes a long way. And it'll keep my boyfriend away right now. I could use that," she suggested innocently.

Stark smiled, "Good idea. Let me guess, you're dating Commander Pointy-Ears up on the bridge. Chocolates always repel Vulcans."

"Yep. Unfortunately, I am," she replied. Stark smirked.

"Guess I'll see you around?" he asked.

"Absolutely," she replied quickly. He nodded and slipped out, checking both ways of the hallway before letting the door slide closed behind him.

! #$%^&*())(*&^%$# !

Admiral Alexander Marcus glared at the red-haired woman in front of him. She didn't even flinch from his fury.

"So, Ensign Rushman. Would you care to explain why this report was hidden from me for three hours?" he said coldly. Natalie Rushman merely frowned at him.

"Because I had other duties to attend to. I may be your aide, Admiral, but I was ordered to Starfleet Medical for a regulation check-up," the red-head said calmly.

"Fine," he snapped before turning and stalking into his office. As the door slid shut behind him, he felt her eyes on his back. He turned to his computer screen and flicked the switch to turn it on. He studied the reports on the ship he was building to fight the Klingons in the upcoming war with the warrior species.

"What is that woman hiding?" he asked himself. Ensign Rushman was hiding something alright, but what was it? Why would she so desperately want to hide something from her superior officer? He shrugged and turned back to the reports he was reading. Who cared what the woman was hiding. As long as it didn't affect her productivity.

Natasha Romanoff let a tiny sigh slip free as Marcus stormed into his private office. What the hell was his deal, anyway?

Clint Barton melted out of the shadows, a tool kit in his hand and an engineering uniform replacing his usual outfit he wore. He looked very displeased with his current choice of attire.

"What is it?" he asked quietly after setting up a device to nullify all listening devices in the area. She looked at him as if he were actually as crazy as she usually implied.

"Marcus. I swear he knows something that we don't. It's like he's got something planned but he won't tell anyone else about. He's acting really weird and his recent profile didn't even come close to giving me a full picture of him," Natasha said. Clint shook his head.

"Isn't that just wonderful?" he drawled before putting up the device and getting back to work. He gave her a wink before he walked out.

Alexander Marcus smiled. So this new pair of people in Starfleet were spies, but who sent them and why? Were they here to protect him or harm him? He needed to find out fast, before someone else did first.

! #$%^&*())(*&^%$# !

James Tiberius Kirk frowned at the poor woman in Chekov's seat. She had just confirmed their sudden drop out of warp.

"Chekov, did you just break my ship?" he asked plainly. He heard muffled Russian words through the channel. The poor kid was under so much pressure.

"_Ah, no, Keptin. I-I don't know. Ve noticed a problem and had to drop out of varp before ze varp driwe exploded. Ve came really close to a varp core breech."_

"How far are we from our destination?" he asked Lieutenant Hikaru Sulu at the helm. He shrugged.

"About twenty minutes, sir," he reported.

Jim sighed, "That's twenty minutes in enemy territory that we weren't planning on."

He hit the button for a shipwide broadcast, "This is Captain Kirk speaking. We just dropped out of warp suddenly, as I'm sure you noticed. We're twenty minutes from our destination. We will take the smuggler ship we captured to get Harrison. Let's get the sonuva bitch. Kirk out."

He cut the channel and leaned back, "Uhura, you can speak Klingon right?"

"Yes, sir."

"Good. You're with me. Spock, you too."

The two aforementioned officers followed Kirk to the shuttlebay, where they were met by two security officers.

Kirk tossed them some shirts," Lose the redshirts. If we fail, we don't want anyone to connect this with Starfleet."

"Yes sir," the two men mumbled. They both pulled their shirts off right there and dropped them on the deck, pulling on the shirts Kirk had handed them. They all got on the ship and prepared to leave the _Enterprise_.

! #$%^&*())(*&^%$# !

Tony Stark checked to make sure that the various pieces of the Iron Man armor were concealed under various parts of equipment in the small smuggling ship. Kirk still hadn't recognized him yet. As they took off, he only paid slight attention to the conversation going on between Lieutenant Uhura and Commander Spock. He gave a slight smirk when Uhura brought Kirk into the conversation.

When they were attacked by the Klingon bird-of-prey, he hung on for dear life as they went through a gap far too small for anyone to logically fit through. Yet Kirk did, by turning the ship on its side. Uhura yelped slightly and Spock favored Kirk with a Vulcan glare.

On the other side of the gap, they were ambushed by three Klingon birds-of-prey. They were forced to land and it was Lieutenant Uhura who was forced to go outside because she was the only one who could speak Klingon.

Tony watched in silence as Kirk handed them all weapons, including Spock. They all knew that a fight was coming. And it did. As the Klingon grabbed Uhura and was about to gut her, he was shot by a strange man on a ledge with two guns. The four men raced out of the craft and joined the fight. Tony swore in Andorian, something Rhodey had taught him a long time ago.

"JARVIS!" he yelled to the AI system, who controlled his suit. The pieces rattled their containment spaces as they flew out and attached to Tony. He managed to duck out of the way of a Klingon bat'leth in time as the large weapon came swinging down to cut him in half.

"What the hell?" the other security guy said when he saw Tony fly up and start blasting Klingons with his repulsor rays. But even his tech could only go so far. A stray phaser shot caught his back and sent him plummeting to the ground.

"Well, Mr. Stark," Kirk said, "This makes twice now you've snuck onto my ship. How did I not recognize you?"

Tony went back to back with the younger man for a split second before spinning off and punching a Klingon in the face.

"JARVIS had something to do with that. He manipulated a holographic image to envelope me and hide who I really am by projecting the image of a green crewman fresh out of the Academy," Tony admitted. Kirk grunted as he ducked from a Klingon fist and retaliated with a swing of his own.

"Well then. Maybe you could use that to help us!" he yelled over the sound of a Klingon bird-of-prey being destroyed by the strange man on the ledge, who jumped down and finished the fight. Tony, Kirk, Spock, and Uhura gathered in a small group. Kirk muttered a rather vulgar curse as he stood up.

"Who are you?" the strange man asked, his voice identifying him as someone from Europe or the Alpha Centauri system.

"Captain James T. Kirk of the _USS Enterprise_," Kirk replied.

"Captain," the man murmured. In the split second afterwards, he threw his weapon down, "I surrender."

"What?" Kirk asked, confused as to what had just happened.

"I surrender," he said simply.

Kirk was silent for a minute before replying, "On behalf of Christopher Pike and all the other innocent men and women you murdered, I accept your surrender, Harrison."

He turned slightly to the side before spinning around and proceeding to punch Harrison in the face repeatedly. Spock looked like it was painful to watch. Uhura gasped and Tony simply stared. How was Harrison not even bruising under the assault?

When Kirk finally stopped, Harrison was standing upright and without a single bruise to even give away that Kirk had just went berserk on him.

! #$%^&*())(*&^%$# !

Captain T'Les Reed of the _USS Dominant_ stared at the screen on her desk. Admiral Andrew Bennett had just told her that one of her closest friends had been killed by a terrorist.

"I'm sorry, Captain Reed. We sent Kirk after this man. He can make him pay. Bennett out," he said before the link was cut. T'Les sat there in shock before wandering out onto the bridge.

Her first officer, Commander Havithress ch'Tlanek instantly noticed something was wrong. They had known each other, the chief engineer Lieutenant Commander Chola, and Chris Pike for fifteen years now.

"What is it?" Thress asked as she sat down heavily. She ignored him for a minute while she opened a channel to Chola, the Tellarite engineer.

"_Chola here, Captain,_" the engineer replied.

T'Les took a deep breath before replying, "Chola, Thress, Admiral Bennett just contacted me. Chris was killed by a terrorist. The same guy who blew up the archive in London. I'm sorry."

Chola cut the channel without replying. T'Les knew that the blunt Tellarite was delivering the news to her engineering staff. Thress sat down at his tactical station and swore in Andorian.

T'Les opened a channel for a shipwide broadcast.

"This is Captain Reed speaking. Some of you may already know, but I just received some startling news from Admiral Bennett on Earth. You all know what happened in London a few days ago. The same man attacked the mandated emergency meeting and killed several officers, including Admiral Christopher Pike. The _Enterprise_ was sent to bring this asshole back to Earth so he can be imprisoned by Starfleet. Let's hope Kirk can catch this man and bring him to justice. Reed out."

The bridge crew stared at her. She slumped in her chair and put a hand to her eyes, which were starting to tear up.

"Helm, best speed for the Klingon Neutral Zone. I'm ordering the entire crew to go against Starfleet Command's orders. Let's help Kirk catch this man. He certainly doesn't have to do it on his own, like he did with Nero."

No one protested, not even her communications officer, Lieutenant Commander Stinson. They all complied and the ship went to warp, towards the darkness that was waiting to engulf the entire Federation.

**AN- Pardon the OCs here. For those of you who haven't realized it by now, I don't follow canon to the letter. I like to create new realities for the fandoms I work with. Well, see y'all next time.**


End file.
